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Borgstahl G, Azadmanesh J, Slobodnik K, Struble L, Lutz W, Coates L, Weiss K, Myles D, Kroll T. Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. RESEARCH SQUARE 2024:rs.3.rs-3880128. [PMID: 38405788 PMCID: PMC10889052 DOI: 10.21203/rs.3.rs-3880128/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting O 2 ∙ - to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.
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Azadmanesh J, Slobodnik K, Struble LR, Lutz WE, Coates L, Weiss KL, Myles DAA, Kroll T, Borgstahl GEO. Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577433. [PMID: 38328249 PMCID: PMC10849630 DOI: 10.1101/2024.01.26.577433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Human manganese superoxide dismutase (MnSOD) is a crucial oxidoreductase that maintains the vitality of mitochondria by converting O 2 ●- to O 2 and H 2 O 2 with proton-coupled electron transfers (PCETs). Since changes in mitochondrial H 2 O 2 concentrations are capable of stimulating apoptotic signaling pathways, human MnSOD has evolutionarily gained the ability to be highly inhibited by its own product, H 2 O 2 . A separate set of PCETs is thought to regulate product inhibition, though mechanisms of PCETs are typically unknown due to difficulties in detecting the protonation states of specific residues that coincide with the electronic state of the redox center. To shed light on the underlying mechanism, we combined neutron diffraction and X-ray absorption spectroscopy of the product-bound, trivalent, and divalent states to reveal the all-atom structures and electronic configuration of the metal. The data identifies the product-inhibited complex for the first time and a PCET mechanism of inhibition is constructed.
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Lutz WE, Azadmanesh J, Lovelace JJ, Kolar C, Coates L, Weiss KL, Borgstahl GEO. Perfect Crystals: microgravity capillary counterdiffusion crystallization of human manganese superoxide dismutase for neutron crystallography. NPJ Microgravity 2023; 9:39. [PMID: 37270576 PMCID: PMC10238240 DOI: 10.1038/s41526-023-00288-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
The NASA mission Perfect Crystals used the microgravity environment on the International Space Station (ISS) to grow crystals of human manganese superoxide dismutase (MnSOD)-an oxidoreductase critical for mitochondrial vitality and human health. The mission's overarching aim is to perform neutron protein crystallography (NPC) on MnSOD to directly visualize proton positions and derive a chemical understanding of the concerted proton electron transfers performed by the enzyme. Large crystals that are perfect enough to diffract neutrons to sufficient resolution are essential for NPC. This combination, large and perfect, is hard to achieve on Earth due to gravity-induced convective mixing. Capillary counterdiffusion methods were developed that provided a gradient of conditions for crystal growth along with a built-in time delay that prevented premature crystallization before stowage on the ISS. Here, we report a highly successful and versatile crystallization system to grow a plethora of crystals for high-resolution NPC.
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Affiliation(s)
- William E Lutz
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Jahaun Azadmanesh
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Jeffrey J Lovelace
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Carol Kolar
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Gloria E O Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE, 68198-6805, USA.
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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The structure-function relationships and physiological roles of MnSOD mutants. Biosci Rep 2022; 42:231385. [PMID: 35662317 PMCID: PMC9208312 DOI: 10.1042/bsr20220202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/10/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
In this review, we focus on understanding the structure–function relationships of numerous manganese superoxide dismutase (MnSOD) mutants to investigate the role that various amino acids play to maintain enzyme quaternary structure or the active site structure, catalytic potential and metal homeostasis in MnSOD, which is essential to maintain enzyme activity. We also observe how polymorphisms of MnSOD are linked to pathologies and how post-translational modifications affect the antioxidant properties of MnSOD. Understanding how modified forms of MnSOD may act as tumor promoters or suppressors by altering the redox status in the body, ultimately aid in generating novel therapies that exploit the therapeutic potential of mutant MnSODs or pave the way for the development of synthetic SOD mimics.
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Azadmanesh J, Borgstahl GEO. A Review of the Catalytic Mechanism of Human Manganese Superoxide Dismutase. Antioxidants (Basel) 2018; 7:antiox7020025. [PMID: 29385710 PMCID: PMC5836015 DOI: 10.3390/antiox7020025] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/13/2018] [Accepted: 01/26/2018] [Indexed: 12/15/2022] Open
Abstract
Superoxide dismutases (SODs) are necessary antioxidant enzymes that protect cells from reactive oxygen species (ROS). Decreased levels of SODs or mutations that affect their catalytic activity have serious phenotypic consequences. SODs perform their bio-protective role by converting superoxide into oxygen and hydrogen peroxide by cyclic oxidation and reduction reactions with the active site metal. Mutations of SODs can cause cancer of the lung, colon, and lymphatic system, as well as neurodegenerative diseases such as Parkinson's disease and amyotrophic lateral sclerosis. While SODs have proven to be of significant biological importance since their discovery in 1968, the mechanistic nature of their catalytic function remains elusive. Extensive investigations with a multitude of approaches have tried to unveil the catalytic workings of SODs, but experimental limitations have impeded direct observations of the mechanism. Here, we focus on human MnSOD, the most significant enzyme in protecting against ROS in the human body. Human MnSOD resides in the mitochondrial matrix, the location of up to 90% of cellular ROS generation. We review the current knowledge of the MnSOD enzymatic mechanism and ongoing studies into solving the remaining mysteries.
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Affiliation(s)
- Jahaun Azadmanesh
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA.
| | - Gloria E O Borgstahl
- Department of Biochemistry and Molecular Biology, 985870 Nebraska Medical Center, Omaha, NE 68198-5870, USA.
- Eppley Institute for Cancer and Allied Diseases, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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Substrate-analog binding and electrostatic surfaces of human manganese superoxide dismutase. J Struct Biol 2017; 199:68-75. [PMID: 28461152 DOI: 10.1016/j.jsb.2017.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/10/2017] [Accepted: 04/27/2017] [Indexed: 01/22/2023]
Abstract
Superoxide dismutases (SODs) are enzymes that play a key role in protecting cells from toxic oxygen metabolites by disproportionation of two molecules of superoxide into molecular oxygen and hydrogen peroxide via cyclic reduction and oxidation at the active site metal. The azide anion is a potent competitive inhibitor that binds directly to the metal and is used as a substrate analog to superoxide in studies of SOD. The crystal structure of human MnSOD-azide complex was solved and shows the putative binding position of superoxide, providing a model for binding to the active site. Azide is bound end-on at the sixth coordinate position of the manganese ion. Tetrameric electrostatic surfaces were calculated incorporating accurate partial charges for the active site in three states, including a state with superoxide coordinated to the metal using the position of azide as a model. These show facilitation of the anionic ligand to the active site pit via a 'valley' of positively-charged surface patches. Surrounding ridges of negative charge help guide the superoxide anion. Within the active site pit, Arg173 and Glu162 further guide and align superoxide for efficient catalysis. Superoxide coordination at the sixth position causes the electrostatic surface of the active site pit to become nearly neutral. A model for electrostatic-mediated diffusion, and efficient binding of superoxide for catalysis is presented.
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LC-MS/MS Analysis Unravels Deep Oxidation of Manganese Superoxide Dismutase in Kidney Cancer. Int J Mol Sci 2017; 18:ijms18020319. [PMID: 28165386 PMCID: PMC5343855 DOI: 10.3390/ijms18020319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/11/2017] [Accepted: 01/25/2017] [Indexed: 01/11/2023] Open
Abstract
Manganese superoxide dismutase (MNSOD) is one of the major scavengers of reactive oxygen species (ROS) in mitochondria with pivotal regulatory role in ischemic disorders, inflammation and cancer. Here we report oxidative modification of MNSOD in human renal cell carcinoma (RCC) by the shotgun method using data-dependent liquid chromatography tandem mass spectrometry (LC-MS/MS). While 5816 and 5571 proteins were identified in cancer and adjacent tissues, respectively, 208 proteins were found to be up- or down-regulated (p < 0.05). Ontological category, interaction network and Western blotting suggested a close correlation between RCC-mediated proteins and oxidoreductases such as MNSOD. Markedly, oxidative modifications of MNSOD were identified at histidine (H54 and H55), tyrosine (Y58), tryptophan (W147, W149, W205 and W210) and asparagine (N206 and N209) residues additional to methionine. These oxidative insults were located at three hotspots near the hydrophobic pocket of the manganese binding site, of which the oxidation of Y58, W147 and W149 was up-regulated around three folds and the oxidation of H54 and H55 was detected in the cancer tissues only (p < 0.05). When normalized to MNSOD expression levels, relative MNSOD enzymatic activity was decreased in cancer tissues, suggesting impairment of MNSOD enzymatic activity in kidney cancer due to modifications. Thus, LC-MS/MS analysis revealed multiple oxidative modifications of MNSOD at different amino acid residues that might mediate the regulation of the superoxide radicals, mitochondrial ROS scavenging and MNSOD activity in kidney cancer.
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Detection and Characterisation of Mutations Responsible for Allele-Specific Protein Thermostabilities at the Mn-Superoxide Dismutase Gene in the Deep-Sea Hydrothermal Vent Polychaete Alvinella pompejana. J Mol Evol 2013; 76:295-310. [DOI: 10.1007/s00239-013-9559-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 03/27/2013] [Indexed: 12/19/2022]
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Synthesis of a Novel Rigid Artificial Superoxide Dismutase Based on Modified Hollow Mesoporous Silica Microspheres. J Inorg Organomet Polym Mater 2011. [DOI: 10.1007/s10904-011-9547-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Bafana A, Dutt S, Kumar A, Kumar S, Ahuja PS. The basic and applied aspects of superoxide dismutase. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2010.11.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Facile and scalable synthesis of a novel rigid artificial superoxide dismutase based on modified hollow mesoporous silica microspheres. Biosens Bioelectron 2011; 26:1936-41. [DOI: 10.1016/j.bios.2010.06.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 05/26/2010] [Accepted: 06/28/2010] [Indexed: 11/22/2022]
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Abreu IA, Cabelli DE. Superoxide dismutases-a review of the metal-associated mechanistic variations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:263-74. [PMID: 19914406 DOI: 10.1016/j.bbapap.2009.11.005] [Citation(s) in RCA: 316] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 11/04/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
Superoxide dismutases are enzymes that function to catalytically convert superoxide radical to oxygen and hydrogen peroxide. These enzymes carry out catalysis at near diffusion controlled rate constants via a general mechanism that involves the sequential reduction and oxidation of the metal center, with the concomitant oxidation and reduction of superoxide radicals. That the catalytically active metal can be copper, iron, manganese or, recently, nickel is one of the fascinating features of this class of enzymes. In this review, we describe these enzymes in terms of the details of their catalytic properties, with an emphasis on the mechanistic differences between the enzymes. The focus here will be concentrated mainly on two of these enzymes, copper, zinc superoxide dismutase and manganese superoxide dismutase, and some relatively subtle variations in the mechanisms by which they function.
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Affiliation(s)
- Isabel A Abreu
- Plant Genetic Engineering Group, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa, Quinta do Marquês, 2784-505 Oeiras, Portugal
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Grey M, Yainoy S, Prachayasittikul V, Bülow L. A superoxide dismutase-human hemoglobin fusion protein showing enhanced antioxidative properties. FEBS J 2009; 276:6195-203. [DOI: 10.1111/j.1742-4658.2009.07323.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Herbst RW, Guce A, Bryngelson PA, Higgins KA, Ryan KC, Cabelli DE, Garman SC, Maroney MJ. Role of conserved tyrosine residues in NiSOD catalysis: a case of convergent evolution. Biochemistry 2009; 48:3354-69. [PMID: 19183068 PMCID: PMC3690555 DOI: 10.1021/bi802029t] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Superoxide dismutases rely on protein structural elements to adjust the redox potential of the metallocenter to an optimum value near 300 mV (vs NHE), to provide a source of protons for catalysis, and to control the access of anions to the active site. These aspects of the catalytic mechanism are examined herein for recombinant preparations of the nickel-dependent SOD (NiSOD) from Streptomyces coelicolor and for a series of mutants that affect a key tyrosine residue, Tyr9 (Y9F-, Y62F-, Y9F/Y62F-, and D3A-NiSOD). Structural aspects of the nickel sites are examined by a combination of EPR and X-ray absorption spectroscopies, and by single-crystal X-ray diffraction at approximately 1.9 A resolution in the case of Y9F- and D3A-NiSODs. The functional effects of the mutations are examined by kinetic studies employing pulse radiolytic generation of O2- and by redox titrations. These studies reveal that although the structure of the nickel center in NiSOD is unique, the ligand environment is designed to optimize the redox potential at 290 mV and results in the oxidation of 50% of the nickel centers in the oxidized hexamer. Kinetic investigations show that all of the mutant proteins have considerable activity. In the case of Y9F-NiSOD, the enzyme exhibits saturation behavior that is not observed in wild-type (WT) NiSOD and suggests that release of peroxide is inhibited. The crystal structure of Y9F-NiSOD reveals an anion binding site that is occupied by either Cl- or Br- and is located close to but not within bonding distance of the nickel center. The structure of D3A-NiSOD reveals that in addition to affecting the interaction between subunits, this mutation repositions Tyr9 and leads to altered chemistry with peroxide. Comparisons with Mn(SOD) and Fe(SOD) reveal that although different strategies for adjusting the redox potential and supply of protons are employed, NiSOD has evolved a similar strategy for controlling the access of anions to the active site.
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Affiliation(s)
- Robert W. Herbst
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Abigail Guce
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Peter A. Bryngelson
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Khadine A. Higgins
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Kelly C. Ryan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Diane E. Cabelli
- Department of Chemistry. Brookhaven National Laboratory, Upton, New York 11973
| | - Scott C. Garman
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003,
| | - Michael J. Maroney
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003,
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